Without a script/storyboard it's hard to be specific, but off the top of my head here's what I would do:
Cut the chroma footage of the actor in PremierePro.
Use Dynamic Link to work on each shot in AE to do the compositing and animation. Make sure you keep the AE project open once you start working on animations and compositing (or that you open it before you select in Premiere your next shot). This way you will have all shots in the same project as separate comps and you can use elements from one comp in the others (like UI elements, animations that may apply to more than one shot...etc).

I have yet to make well use of dynamic links. That is something I've been putting of learning.

So far I have been editing in Premiere, and making smaller (10-20 second) clips of each section that needs animation. Then copying the section to a dummy sequence (blank sequence). Once inside I would copy/paste the sequence into After Effects, animate to the audio, render, then import the rendered video back to Premiere's timeline. Cutting sections in Premiere seemed like a good way to know exactly which parts will need to be keyed as well, instead of keying ALL of the footage.